8XAG | pdb_00008xag

Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone H3.3K27me3 peptide

PDB DOI: https://doi.org/10.2210/pdb8XAG/pdb

Classification: GENE REGULATION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-04 Released: 2024-12-04
Deposition Author(s): Liu, Y., Huang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.250 (Depositor), 0.251 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone H3.3K27me3 peptide

Liu, Y., Huang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 17.12 kDa
Atom Count: 1,269
Modeled Residue Count: 132
Deposited Residue Count: 148
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromo domain-containing protein LHP1	A, B	66	Arabidopsis thaliana	Mutation(s): 0 Gene Names: LHP1
UniProt
Find proteins for Q946J8 (Arabidopsis thaliana) Explore Q946J8 Go to UniProtKB: Q946J8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q946J8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
histone H3.3K27me3 peptide	C, D	8	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P59169 (Arabidopsis thaliana) Explore P59169 Go to UniProtKB: P59169
Entity Groups
UniProt Group	P59169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L Query on M3L	C, D	L-PEPTIDE LINKING	C₉ H₂₁ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.250 (Depositor), 0.251 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.37	α = 90
b = 90.623	β = 90
c = 63.574	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171186

Revision History (Full details and data files)

Version 1.0: 2024-12-04
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.